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Impact of Worldviews

Protein Folding

Most people know that in our everyday world, two opposite conditions cannot both be true at the same time. One wishes however that modern biologists would recognize this fact.

Consider the issue of protein folding. Since the 1960s, biologists have understood that the shape of a protein is essential to its function. The irreducible molecular machines which are so important to the functioning of the living cell, are made up of precisely shaped proteins. And the shape is genetically controlled by the sequence of nucleotides in the DNA of the cell. You might say that all biologists today know that. What has concerned some scientists recently however is that there are proteins with similar shapes but the controlling nucleotide sequences are very different. Could a DNA sequence change but the protein shape remain the same? This is the evolutionary explanation that some scientists are promoting.

It is now about sixty years since scientists first proposed that the order of the amino acids on the protein strand is what determines how the chain will fold into its correct shape. Three people, Stanford Moore, William Stein and Christian Anfinsen won the 1972 Nobel Prize in Chemistry for this explanation. This however is just the beginning of understanding proteins. The problem is that even a relatively small protein can collapse into a huge number of possible shapes. It depends upon which folds come first, what the final shape is. Obviously also, it is much harder to figure out interactions in a large protein. The factors determining the order of folding involve the shapes of the component amino acids along the strand and the electrical charges on these component parts.

Scientists have long sought to discover all the ways that strings of amino acids could potentially fold and they also want to know the ways in which they actually do fold. The Protein Structure Initiative was set up in 2000 to seek a complete understanding of elaborate protein folds. Using fancy techniques, this center, based in Bethesda Maryland, sought to map all the ways that a protein can fold. Some critics complained that in the first ten years, this laboratory studied mainly easier proteins of little biological significance.  Thus of 5000 proteins for which folds had been mapped, only 128 were human proteins. Human proteins tend to be larger and more difficult to work with than proteins from some microbes.

Obviously, the use of supercomputing power is a must for studying protein structure. With all the complexities of three-dimensional shape in the finished protein and long chains of amino acids needing to be appropriated collapsed, it typically took a month of supercomputing time to solve one structure.  Scientists at the time (about 2010) thought that this approach might show promise if we had supercomputers 1000 times faster than were then available! Fast forward to amazing revelations in 2022.  (But first we need to consider further the significance of precision in protein folding).

All these computer studies of protein structure are based on the idea that DNA sequence determines the structure and function of proteins. Mutations in the gene sequence often exert significant results. For example, Nobel prize winner Jennifer Doudna discusses how a change in one nucleotide, out of more than 400 in the beta-globin molecule (major part of hemoglobin) results in a change in shape of hemoglobin with potentially serious impacts to human health.  “[I]n sickle cell disease, a genetic disorder of the blood, the seventeenth letter of a gene known as beta-globin is mutated from an A to a T. When translated into amino acids, this mutation results in the amino acid glutamate being replaced by the amino acid valine in a critical region of the hemoglobin protein…. The consequences of this tiny change in protein – a difference of just ten atoms out of more than eight thousand total – are dire.” [Jennifer Doudna and Samuel Sternberg. 2017. A Crack in Creation: the new power to control evolution. Bodley Head. p. 13]  If one small mutation can exert such an impact on shape and function, we can imagine what mutations over hundreds of millions of years might do to a protein’s structure.

Like many fields of science, AI (Artificial Intelligence) is causing great advances in the study of protein folding based on the genetic sequence. Up until now of course, figuring out protein folding and thus its structure, has been a formidable problem. But in July 2021, the London-based firm DeepMind, part of Alphabet (Google’s parent company) made public an artificial intelligence tool called AlphaFold. This software can apparently predict the three-dimensional shape of many proteins from their genetic sequence with, for the most part, impressive accuracy. That same month in 2021, DeepMind announced that it had used the AlphaFold program to predict the structure of nearly every protein made by humans as well as proteins from several other organisms.

So far so good (and exciting!) But in any field of biology, can thoughts of evolution be far behind? Some experts pointed out that comparisons of proteins structure could be interesting in evolutionary comparisons. The scientists already had comparisons of genetic sequences in hand. So, what other information might be relevant? This is where our opposite conditions situation comes into play. The article on AlphaFold declared: “Researchers compare genetic sequences to determine how organisms and their genes are related across species. For distantly related genes, comparisons might fail to turn up evolutionary relatives because the sequences have changed so much. But by comparing proteins structures – which tend to change less rapidly than genetic sequences – researchers might be able to uncover overlooked ancient relationships.” [Ewan Callaway. 2022. What’s Next for the AI Protein-folding Revolution. Nature 604: pp. 234-238.  See p. 236.]

Oh really? Are they saying that there is protein structure which does not change at the same time as the controlling DNA sequence changes? This is the opposite of what scientists have concluded since the 1960s and the opposite of the premises of the AlphaFold study. There are some cases however where scientists believe that there was a common ancestor from which modern organisms descended, but the DNA sequences in the modern organisms are too different to conclude that they had a common origin. Not to worry, the article in Nature insists. We can compare protein shape instead. The structures may be close enough to conclude that these proteins, from separate organisms, once had a common ancestor even if the DNA sequences look different.

A key example of this is the origin of photosynthesis. The process is so complicated that scientists believe that the relevant photosynthetic hardware (molecular machines in the reaction center complex) could only have originated once. However today we see two versions of the reaction center complex. In view of the fact that scientists seek one ancestral core reaction center (and they now see two) the situation has been considered problematic.  Thus: “The origin and extent of distribution of these proteins has been perplexing from a phylogenetic point of view mostly because of extreme sequence divergence.” [Sumedha Sadekar, Jason Raymond and Robert Blankenship. 2006. Conservation of Distantly Related Membrane Proteins: Photosynthetic Reaction Centers Share a Common Structural Core.  Mol. Biol. Evol. 23 (11) 2001-2007. See p. 2001 emphasis mine]   Their solution was: “The reaction center complexes show a remarkable conservation of the core structure of 5 transmembrane helices, strongly implying common ancestry, even though the residual sequence identity is less than 10%.” [p. 2001] and “Phylogenetic trees derived from the structural alignments give insights into the earliest photosynthetic reaction center.”  

So, there we have it. Scientists use sequence similarity to suggest common ancestry. When that doesn’t work, they may yet conclude, based on shape of the protein, that there was common ancestry anyway. Heads you win, tails you win!

 What we see in cases of similar shape and function (but different underlying genetic sequence) is a blueprint for a protein with different amino acids used in its composition. Design is an obvious explanation for this case. On the other hand, sometimes evolutionists attribute this to convergence to explain that evolution is true even if modification with descent (evolution) did not produce what we see. (See Convergence for insect odour receptors which display this situation very dramatically.) In the present case however, evolutionists attribute the cause of common structures to a lengthy process of descent with modification in the DNA, but which left the protein shape and structure unaffected by the long-term process.  The evolutionists are thus promoting opposite explanations for their observations of similar protein structures. Evolution then fails as an explanation. As far as we are concerned, nothing is too hard for God, the creator. He can produce whatever shape of protein molecule He likes, using many alternative DNA sequences.  The situation we see here perfectly demonstrates the power and the work of God, the Creator.

Related Terms

  • Polymer Formation
  • Origin of Life Studies: Abiogenesis
  • Blueprint
  • Convergence
  • Convergence (Specific Example)
  • Photosynthesis